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- SASDEL9: Escherichia coli aerobic fatty acid beta-oxidation trifunctional ... -

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Basic information

Entry
Database: SASBDB / ID: SASDEL9
SampleEscherichia coli aerobic fatty acid beta-oxidation trifunctional enzyme complex
  • Fatty acid oxidation complex subunit alphaBeta oxidation (protein), EcTFE-alpha, Escherichia coli (strain K12)
  • Fatty acid oxidation complex subunit alphaBeta oxidation (protein), EcTFE-alpha, Escherichia coli (strain K12)
  • 3-ketoacyl-CoA thiolase FadA (beta subunit) (protein), EcTFE-beta, Escherichia coli (strain K12)
Function / homology
Function and homology information


fatty acid beta-oxidation multienzyme complex / 3-hydroxybutyryl-CoA epimerase / 3-hydroxybutyryl-CoA epimerase activity / Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / acetyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase activity / long-chain-3-hydroxyacyl-CoA dehydrogenase activity / 3-hydroxyacyl-CoA dehydrogenase / phenylacetate catabolic process ...fatty acid beta-oxidation multienzyme complex / 3-hydroxybutyryl-CoA epimerase / 3-hydroxybutyryl-CoA epimerase activity / Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / acetyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase activity / long-chain-3-hydroxyacyl-CoA dehydrogenase activity / 3-hydroxyacyl-CoA dehydrogenase / phenylacetate catabolic process / enoyl-CoA hydratase / 3-hydroxyacyl-CoA dehydrogenase activity / enoyl-CoA hydratase activity / fatty acid beta-oxidation / NAD+ binding / cytoplasm
Similarity search - Function
Fatty oxidation complex, alpha subunit FadB / Acetyl-CoA C-acyltransferase FadA / 3-hydroxyacyl-CoA dehydrogenase, conserved site / 3-hydroxyacyl-CoA dehydrogenase signature. / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / Thiolase, active site / Thiolases active site. ...Fatty oxidation complex, alpha subunit FadB / Acetyl-CoA C-acyltransferase FadA / 3-hydroxyacyl-CoA dehydrogenase, conserved site / 3-hydroxyacyl-CoA dehydrogenase signature. / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Thiolase / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal / Thiolase, N-terminal domain / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / ClpP/crotonase-like domain superfamily / Thiolase-like / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
3-ketoacyl-CoA thiolase FadA / Fatty acid oxidation complex subunit alpha
Similarity search - Component
Biological speciesEscherichia coli (strain K12) (bacteria)
CitationJournal: Biochem J / Year: 2019
Title: Complementary substrate specificity and distinct quaternary assembly of the aerobic and anaerobic β-oxidation trifunctional enzyme complexes.
Authors: Shiv K Sah-Teli / Mikko J Hynönen / Werner Schmitz / James A Geraets / Jani Seitsonen / Jan Skov Pedersen / Sarah J Butcher / Rik K Wierenga / Rajaram Venkatesan /
Abstract: The trifunctional enzyme (TFE) catalyzes the last three steps of the fatty acid β-oxidation cycle. Two TFEs are present in , EcTFE and anEcTFE. EcTFE is expressed only under aerobic conditions, ...The trifunctional enzyme (TFE) catalyzes the last three steps of the fatty acid β-oxidation cycle. Two TFEs are present in , EcTFE and anEcTFE. EcTFE is expressed only under aerobic conditions, whereas anEcTFE is expressed also under anaerobic conditions, with nitrate or fumarate as the ultimate electron acceptor. The anEcTFE subunits have higher sequence identity with the human mitochondrial TFE (HsTFE) than with the soluble EcTFE. Like HsTFE, here it is found that anEcTFE is a membrane-bound complex. Systematic enzyme kinetic studies show that anEcTFE has a preference for medium- and long-chain enoyl-CoAs, similar to HsTFE, whereas EcTFE prefers short chain enoyl-CoA substrates. The biophysical characterization of anEcTFE and EcTFE shows that EcTFE is heterotetrameric, whereas anEcTFE is purified as a complex of two heterotetrameric units, like HsTFE. The tetrameric assembly of anEcTFE resembles the HsTFE tetramer, although the arrangement of the two anEcTFE tetramers in the octamer is different from the HsTFE octamer. These studies demonstrate that EcTFE and anEcTFE have complementary substrate specificities, allowing for complete degradation of long-chain enoyl-CoAs under aerobic conditions. The new data agree with the notion that anEcTFE and HsTFE are evolutionary closely related, whereas EcTFE belongs to a separate subfamily.
Contact author
  • shiv k. sah-teli (University of Oulu, Finland)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Models

Model #2747
Type: dummy / Radius of dummy atoms: 5.80 A / Symmetry: p1 / Chi-square value: 1.029 / P-value: 0.936796
Search similar-shape structures of this assembly by Omokage search (details)
Model #2748
Type: atomic
Comment: subunits and complex were modeled using swissmodel and coot respectively using 1wdm.pdb as referenc
Chi-square value: 1.357 / P-value: 0.000001
Search similar-shape structures of this assembly by Omokage search (details)

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Sample

SampleName: Escherichia coli aerobic fatty acid beta-oxidation trifunctional enzyme complex
Specimen concentration: 6.2 mg/ml / Entity id: 1432 / 1433 / 1434
BufferName: 20 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES), 120 mM KCl, 2.5 mM DTT
pH: 7.2
Entity #1432Name: EcTFE-alpha / Type: protein
Description: Fatty acid oxidation complex subunit alphaBeta oxidation
Formula weight: 81.206 / Num. of mol.: 1 / Source: Escherichia coli (strain K12) / References: UniProt: P21177
Sequence: MGSSHHHHHH SQDPMLYKGD TLYLDWLEDG IAELVFDAPG SVNKLDTATV ASLGEAIGVL EQQSDLKGLL LRSNKAAFIV GADITEFLSL FLVPEEQLSQ WLHFANSVFN RLEDLPVPTI AAVNGYALGG GCECVLATDY RLATPDLRIG LPETKLGIMP GFGGSVRMPR ...Sequence:
MGSSHHHHHH SQDPMLYKGD TLYLDWLEDG IAELVFDAPG SVNKLDTATV ASLGEAIGVL EQQSDLKGLL LRSNKAAFIV GADITEFLSL FLVPEEQLSQ WLHFANSVFN RLEDLPVPTI AAVNGYALGG GCECVLATDY RLATPDLRIG LPETKLGIMP GFGGSVRMPR MLGADSALEI IAAGKDVGAD QALKIGLVDG VVKAEKLVEG AKAVLRQAIN GDLDWKAKRQ PKLEPLKLSK IEATMSFTIA KGMVAQTAGK HYPAPITAVK TIEAAARFGR EEALNLENKS FVPLAHTNEA RALVGIFLND QYVKGKAKKL TKDVETPKQA AVLGAGIMGG GIAYQSAWKG VPVVMKDIND KSLTLGMTEA AKLLNKQLER GKIDGLKLAG VISTIHPTLD YAGFDRVDIV VEAVVENPKV KKAVLAETEQ KVRQDTVLAS NTSTIPISEL ANALERPENF CGMHFFNPVH RMPLVEIIRG EKSSDETIAK VVAWASKMGK TPIVVNDCPG FFVNRVLFPY FAGFSQLLRD GADFRKIDKV MEKQFGWPMG PAYLLDVVGI DTAHHAQAVM AAGFPQRMQK DYRDAIDALF DANRFGQKNG LGFWRYKEDS KGKPKKEEDA AVEDLLAEVS QPKRDFSEEE IIARMMIPMV NEVVRCLEEG IIATPAEADM ALVYGLGFPP FHGGAFRWLD TLGSAKYLDM AQQYQHLGPL YEVPEGLRNK ARHNEPYYPP VEPARPVGDL KTA
Entity #1433Name: EcTFE-alpha / Type: protein
Description: Fatty acid oxidation complex subunit alphaBeta oxidation
Formula weight: 81.206 / Num. of mol.: 1 / Source: Escherichia coli (strain K12) / References: UniProt: P21177
Sequence: MGSSHHHHHH SQDPMLYKGD TLYLDWLEDG IAELVFDAPG SVNKLDTATV ASLGEAIGVL EQQSDLKGLL LRSNKAAFIV GADITEFLSL FLVPEEQLSQ WLHFANSVFN RLEDLPVPTI AAVNGYALGG GCECVLATDY RLATPDLRIG LPETKLGIMP GFGGSVRMPR ...Sequence:
MGSSHHHHHH SQDPMLYKGD TLYLDWLEDG IAELVFDAPG SVNKLDTATV ASLGEAIGVL EQQSDLKGLL LRSNKAAFIV GADITEFLSL FLVPEEQLSQ WLHFANSVFN RLEDLPVPTI AAVNGYALGG GCECVLATDY RLATPDLRIG LPETKLGIMP GFGGSVRMPR MLGADSALEI IAAGKDVGAD QALKIGLVDG VVKAEKLVEG AKAVLRQAIN GDLDWKAKRQ PKLEPLKLSK IEATMSFTIA KGMVAQTAGK HYPAPITAVK TIEAAARFGR EEALNLENKS FVPLAHTNEA RALVGIFLND QYVKGKAKKL TKDVETPKQA AVLGAGIMGG GIAYQSAWKG VPVVMKDIND KSLTLGMTEA AKLLNKQLER GKIDGLKLAG VISTIHPTLD YAGFDRVDIV VEAVVENPKV KKAVLAETEQ KVRQDTVLAS NTSTIPISEL ANALERPENF CGMHFFNPVH RMPLVEIIRG EKSSDETIAK VVAWASKMGK TPIVVNDCPG FFVNRVLFPY FAGFSQLLRD GADFRKIDKV MEKQFGWPMG PAYLLDVVGI DTAHHAQAVM AAGFPQRMQK DYRDAIDALF DANRFGQKNG LGFWRYKEDS KGKPKKEEDA AVEDLLAEVS QPKRDFSEEE IIARMMIPMV NEVVRCLEEG IIATPAEADM ALVYGLGFPP FHGGAFRWLD TLGSAKYLDM AQQYQHLGPL YEVPEGLRNK ARHNEPYYPP VEPARPVGDL KTA
Entity #1434Name: EcTFE-beta / Type: protein / Description: 3-ketoacyl-CoA thiolase FadA (beta subunit) / Formula weight: 40.876 / Num. of mol.: 2 / Source: Escherichia coli (strain K12) / References: UniProt: P21151
Sequence: MEQVVIVDAI RTPMGRSKGG AFRNVRAEDL SAHLMRSLLA RNPALEAAAL DDIYWGCVQQ TLEQGFNIAR NAALLAEVPH SVPAVTVNRL CGSSMQALHD AARMIMTGDA QACLVGGVEH MGHVPMSHGV DFHPGLSRNV AKAAGMMGLT AEMLARMHGI SREMQDAFAA ...Sequence:
MEQVVIVDAI RTPMGRSKGG AFRNVRAEDL SAHLMRSLLA RNPALEAAAL DDIYWGCVQQ TLEQGFNIAR NAALLAEVPH SVPAVTVNRL CGSSMQALHD AARMIMTGDA QACLVGGVEH MGHVPMSHGV DFHPGLSRNV AKAAGMMGLT AEMLARMHGI SREMQDAFAA RSHARAWAAT QSAAFKNEII PTGGHDADGV LKQFNYDEVI RPETTVEALA TLRPAFDPVN GMVTAGTSSA LSDGAAAMLV MSESRAHELG LKPRARVRSM AVVGCDPSIM GYGPVPASKL ALKKAGLSAS DIGVFEMNEA FAAQILPCIK DLGLIEQIDE KINLNGGAIA LGHPLGCSGA RISTTLLNLM ERKDVQFGLA TMCIGLGQGI ATVFERV

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Experimental information

BeamInstrument name: Diamond Light Source B21 / City: Didcot / 国: UK / Shape: 1 x 5 mm / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.1 Å / Dist. spec. to detc.: 4.014 mm
DetectorName: Pilatus 2M
Scan
Title: Escherichia coli aerobic fatty acid beta-oxidation trifunctional enzyme complex
Measurement date: May 30, 2017 / Storage temperature: 4 °C / Cell temperature: 20 °C / Exposure time: 3 sec. / Number of frames: 540 / Unit: 1/A /
MinMax
Q0.0167 0.1913
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 692 /
MinMax
Q0.0166657 0.173243
P(R) point1 692
R0 160.3
Result
Type of curve: sec /
ExperimentalPorod
MW233 kDa253 kDa
Volume-406 nm3

P(R)GuinierGuinier error
Forward scattering, I00.06542 0.06559 0.0005
Radius of gyration, Rg4.59 nm4.612 nm0.04

MinMax
D-16.04
Guinier point1 51

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